The main purpose of this study was to investigate natural infection by Leishmania chagasi in female sand flies in a visceral leishmaniasis (VL) focus on São Luís Island, Maranhão State, Brazil. Molecular analysis by polymerase chain reaction (PCR) was applied to determine the rate of natural infection of Lutzomyia longipalpis by L. chagasi in areas of old and recent human settlement on São Luís Island. Based on a sample of 800 female specimens captured from March to August 2005, the natural infection rate was 1.25% in an area of old settlement and 0.25% in two recently settled areas. Infection of L. longipalpis was detected in both areas, regardless of the number of reported human VL cases, indicating that other factors modulating infection in the wild need to be investigated. The results confirm PCR as a specific technique and an important tool for epidemiological surveillance.